GEO DataSets

(Submitter supplied) Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO) proteins to mediate sequence-specific regulation of diverse biological processes. Here, we combine deep-sequencing and genetic approaches to explore the biogenesis and function of endo-siRNAs in C. elegans. We describe conditional alleles of the dicer-related helicase, drh-3, that abrogate both RNA interference and the biogenesis of endo-siRNAs, called 22G-RNAs. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by genome tiling array

Platform:

GPL5634

2 Samples

Download data: BAR, CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by genome tiling array; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL9269 GPL5634

20 Samples

Download data: BAR, CEL, GFF, TAR

(Submitter supplied) Diverse naturally-occurring small RNA species interact with Argonaute proteins to mediate sequence-specific regulation in animals. In addition to micro-RNAs (miRNAs), which collectively regulate thousands of target mRNAs, other endogenous small RNA species include the Piwi-associated piRNAs that are important for fertility and a less well-characterized class of small RNAs often referred to simply as endo-siRNAs. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL9269

18 Samples

Download data: GFF, TAR

(Submitter supplied) To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19757

39 Samples

Download data: XLSX

(Submitter supplied) Small RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL18245

12 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL19757 GPL18245

69 Samples

Download data

(Submitter supplied) Small RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18245

18 Samples

Download data: TSV

(Submitter supplied) Small RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

21 Samples

Download data: TSV

(Submitter supplied) Small RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

18 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6946

16 Samples

Download data

(Submitter supplied) These datasets examine the association of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) with the PRG-1 protein through co-immunoprecipitation. Two datasets are provided; one sequences small RNAs that co-IP with PRG-1; the other sequences small RNAs from the IP input sample. These RNA samples were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL6946

2 Samples

Download data

(Submitter supplied) These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as described in Ambros et al. (2003) Curr Biol 13:807-18. These datasets were prepared in the Craig C. Mello laboratory. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6946

2 Samples

Download data

(Submitter supplied) These datasets profile the expression of small RNAs with 5p monophosphates and 3p hydroxyls (including miRNAs, 21U-RNAs) in young adult worms from the wt, prg-1 mutant, and fog-2 mutant backgrounds. These datasets were prepared in the Craig C. Mello laboratory using T4 RNA ligase 1. Keywords: miRNA and 21U-RNA discovery and mutant expression profiling

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6946

3 Samples

Download data

(Submitter supplied) These datasets profile the expression of small RNAs with 5p monophosphates and 3p hydroxyls (including miRNAs, 21U-RNAs) across C. elegans development and in dauer, glp-4 mutant, and mixed-stage wt worms. These datasets were prepared in the David P. Bartel laboratory using T4 RNA ligase Rnl2(1-249). Keywords: miRNA and 21U-RNA discovery and developmental expression profiling

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6946

9 Samples

Download data

(Submitter supplied) RNA interference (RNAi) is a phylogenetically widespread gene silencing process triggered by doublestranded RNA (dsRNA). In plants and C. elegans, two distinct populations of small RNAs have been proposed to participate in RNAi : "Primary siRNAs" (derived from Dicer nuclease-mediated cleavage of the original trigger) and "Secondary siRNAs" (additional small RNAs whose synthesis requires an RNA-directed RNA polymerase [RdRP]). more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL4569

1 Sample

Download data: TXT

(Submitter supplied) Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

5 Samples

Download data

(Submitter supplied) The Piwi-piRNA pathway represents a germline specific transposon-defense system. C. elegans Piwi, prg-1, is a non-essential gene and triggers a secondary RNAi response that depends on so-called mutator genes, endo-siRNAs (22G-RNAs) and at least one 22G-RNA-binding Argonaute protein, HRDE-1. Interestingly, through a poorly understood mechanism, silencing of PRG-1 targets can become PRG-1 independent. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15716 GPL18245

33 Samples

Download data: TXT

(Submitter supplied) Piwi Argonautes and Piwi-interacting RNAs (piRNAs) mediate genome defense by targeting transposons. However, many piRNA species lack obvious sequence complementarity to transposons or other loci. For example, only one C. elegans transposon is a known piRNA target. Here we show that, in mutants lacking the Piwi Argonaute PRG-1 and associated piRNAs (21U-RNAs), many silent loci in the germline exhibit increased levels of mRNA expression and depletion of an amplified RNAdependent RNA polymerase (RdRP)-derived species of small RNA termed 22G-RNAs. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

6 Samples

Download data: FA

(Submitter supplied) RNAi-elicited gene silencing is heritable and can persist for multiple generations after its initial induction in C. elegans. However, the mechanism by which parental-acquired trait-specific information from RNAi is inherited by the progenies is not fully understood. Here, we identified a cytoplasmic Argonaute protein, WAGO-4, necessary for the inheritance of RNAi. WAGO-4 exhibits asymmetrical translocation to the germline during early embryogenesis, accumulates at the perinuclear foci in the germline, and is required for the inheritance of exogenous RNAi targeting both germline- and soma-expressed genes. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19757 GPL32326

57 Samples

Download data: TXT